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Nucleic Acids Research, 2003, Vol. 31, No. 15 4450-4460
© 2003 Oxford University Press

Microenvironment analysis and identification of magnesium binding sites in RNA

D. Rey Banatao, Russ B. Altman* and Teri E. Klein

Department of Genetics and Stanford Medical Informatics, 251 Campus Drive, Stanford University, CA 94305, USA

*To whom correspondence should be addressed. Tel: +1 650 725 3394; Fax: +1 650 725 7944; Email: russ.altman{at}stanford.edu

Interactions with magnesium (Mg2+) ions are essential for RNA folding and function. The locations and function of bound Mg2+ ions are difficult to characterize both experimentally and computationally. In particular, the P456 domain of the Tetrahymena thermophila group I intron, and a 58 nt 23s rRNA from Escherichia coli have been important systems for studying the role of Mg2+ binding in RNA, but characteristics of all the binding sites remain unclear. We therefore investigated the Mg2+ binding capabilities of these RNA systems using a computational approach to identify and further characterize their Mg2+ binding sites. The approach is based on the FEATURE algorithm, reported previously for microenvironment analysis of protein functional sites. We have determined novel physicochemical descriptions of site-bound and diffusely bound Mg2+ ions in RNA that are useful for prediction. Electrostatic calculations using the Non-Linear Poisson Boltzmann (NLPB) equation provided further evidence for the locations of site-bound ions. We confirmed the locations of experimentally determined sites and further differentiated between classes of ion binding. We also identified potentially important, high scoring sites in the group I intron that are not currently annotated as Mg2+ binding sites. We note their potential function and believe they deserve experimental follow-up.


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